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BNG supports three rate laws, by way of keywords appended to rule definitions. The currently defined keywords are "Ele" (the default -- elementary mass-action), "Sat", and "MM". We should be able to…
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Queries of BEL or BioPax can (and do) result in multiple equivalent statements, as in the following. They should be handled in some way, either by incrementing the count, or perhaps adding to a list o…
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At some point policies became an argument in the constructor of the PysbAssembler. Wouldn't it make sense to put that back as an argument of make_model? The assembler collects statements and we would …
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Dell says fetch the item, send the item JSON back in with the post - see Dell's pysb package for an example
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Somewhere in the guts of odesolve, parameters with s0, s1, etc as part of their name gets rewritten with y.
```
from pysb import*
from pysb.integrate import odesolve
from pysb import bng
import numpy…
dkoes updated
8 years ago
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internal tracking of session stale should be re-upped here.
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PySB can't do its thing (at least its BNG thing) if it doesn't have write access to the current directory. This is an issue if you are running PySB within a cgi script where you don't want the webserv…
dkoes updated
8 years ago
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I'm trying to follow along with the tutorial. Here's what happens on Ubuntu, OS X, and Centos (sympy 0.7.3, numpy 1.10.0.post2, BioNetGen 2.2.6).
```
In [1]: import mymodel as m
In [2]: from pysb.i…
dkoes updated
8 years ago
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It is quite common for Python modules to have __ version __ constant defined in the root module namespace to enable version checking and tracking.
It seems to be lacking from PySB.
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The BNG code was recently changed to output all rules that generate a given reaction to the NET file (BNG 2.2.5 and earlier only output the last rule detected that generated a reaction). The rules are…